Permission inheritance can be broken in Windows SharePoint Services 3.0
at the site  level, but breaking inheritance of permissions does not
prevent the inheritance of SharePoint Groups, just inheritance of
permissions associated with those groups. The groups  you are seeing
were probably created  by the site collection owner. Although the groups
are visible in your site and you can't see the membership, you should be
able to control what rights those groups have. If you remove all the
rights from the group  they should disappear from your interface. You
can add them back by using the AddUser command and typing in the name of
the SharePoint group.

I have looked at the
permission levels of these sharepoint  groups and surprisingly all of
them have no access on my team  site. So I have edited the Quick
Launch Bar in "People and Groups" page and removed the orphan
sharepoint groups. I have a small question here though. Now can the
site collection administrator change the group  settings of any
sharepoint group in the site  collection (though he is not the
specified group owner)? Please let me know.

If the group  settings are set for only the Group owner  to add members
then I don't think that even the site  collection admin can add members
to the group. However, I know they can adjust the permissions on the
group anywhere in the site collection. Since they are the site
collection admin there is no way to prevent that. But I know that users
with Full Control to a group can't add members if the settings are set
to only the Group owner adding members. I suspect that will apply to
the site collection admins also.